Lorentz Contraction: What really Contracts?

OK I've been reading up on Lorentz contractions in special relativity and i have been wondering about something for a while now. When a Lorentz contraction occurs what actually contracts? the space between the atoms? (because we are 99% space) the actual atoms themselves? or the distance between the strong force?(or possible now the gravitational force due to the Schwarzschild proton)

I would appreciate some incite into this question because to my understanding everyone i ask and everywhere i look it just says the "Object" contracts and it gives me the equation to find the factor of the contraction. It doesnt really tell me what the contraction is only that it happens.

As you approach the speed of light in your spaceship, the universe as observed by you will squash in the direction of your travel. The distance to the target star will shrink and the star itself will flatten into a disc. If you could measure atoms whizzing by, the atoms would be flattened in the direction of your travel.

Simple answer "everything"
Everything contacts which is why you can't tell, any ruler or physical process you would use to measure the contraction also contracts - this is a very important point - relativity says you can't tell if you are moving, so you can't use contraction to tell if you are moving - so the contraction must happen in a way to have no measurable effects.

I've never liked thinking of it as a contraction but prefer to think of it as a rotation of the body in the space-time plane. Its the four dimensional version of taking a rod and turning it a bit from your perspective...can look shorter.